chr13:43883789:A>G Detail (hg38) (LACC1, CCDC122)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr13:44,457,925-44,457,925 View the variant detail on this assembly version. |
| hg38 | chr13:43,883,789-43,883,789 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_153218.2:c.760A>G | NP_694950.2:p.Ile254Val |
| NM_001128303.1:c.760A>G | NP_001121775.1:p.Ile254Val | |
| Ensemble | ENST00000325686.7:c.760A>G | ENST00000325686.7:p.Ile254Val |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.329 |
| ToMMo:0.336 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.312 |
Prediction
ClinVar
| Clinical Significance |
Benign
|
| Review star |  |
| Show details | |
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Benign
|
2021-08-19 | criteria provided, single submitter | Juvenile arthritis due to defect in LACC1 |
germline
|
Detail |
| Uncertain risk allele | 2022-06-10 | no assertion criteria provided | Leprosy, susceptibility to, 1 |
inherited
|
Detail |
|
Benign
|
2024-01-24 | criteria provided, single submitter | not specified |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.002 | Behcet Syndrome | [Genome-wide association study identifies variants in the MHC class I, IL10, and... | GAD | 20622878 | Detail |
| 0.009 | ulcerative colitis | SNP-SNP interaction analyses showed that the combination of SNPs in the PTPN22 (... | BeFree | 23974994 | Detail |
| 0.003 | ulcerative colitis | SNP-SNP interaction analyses showed that the combination of SNPs in the PTPN22 (... | BeFree | 23974994 | Detail |
| 0.126 | leprosy | Genomewide association study of leprosy. | GWASCAT | 20018961 | Detail |
| 0.130 | Crohn Disease | [Genome-wide association defines more than 30 distinct susceptibility loci for C... | GAD | 18587394 | Detail |
| 0.126 | leprosy | [Variants of genes in the NOD2-mediated signaling pathway (which regulates the i... | GAD | 20018961 | Detail |
| 0.130 | Crohn Disease | Genome-wide association defines more than 30 distinct susceptibility loci for Cr... | GWASCAT | 18587394 | Detail |
| 0.130 | Crohn Disease | Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's diseas... | GWASCAT | 21102463 | Detail |
| 0.130 | Crohn Disease | Host-microbe interactions have shaped the genetic architecture of inflammatory b... | GWASCAT | 23128233 | Detail |
| 0.126 | leprosy | NA | GAD | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_153218.4(LACC1):c.760A>G (p.Ile254Val) AND Juvenile arthritis due to defect in LACC1 | ClinVar | Detail |
| NM_153218.4(LACC1):c.760A>G (p.Ile254Val) AND Leprosy, susceptibility to, 1 | ClinVar | Detail |
| NM_153218.4(LACC1):c.760A>G (p.Ile254Val) AND not specified | ClinVar | Detail |
| [Genome-wide association study identifies variants in the MHC class I, IL10, and IL23R-IL12RB2 regio... | DisGeNET | Detail |
| SNP-SNP interaction analyses showed that the combination of SNPs in the PTPN22 (rs2476601) and C13or... | DisGeNET | Detail |
| SNP-SNP interaction analyses showed that the combination of SNPs in the PTPN22 (rs2476601) and C13or... | DisGeNET | Detail |
| Genomewide association study of leprosy. | DisGeNET | Detail |
| [Genome-wide association defines more than 30 distinct susceptibility loci for Crohn\'s disease.] | DisGeNET | Detail |
| [Variants of genes in the NOD2-mediated signaling pathway (which regulates the innate immune respons... | DisGeNET | Detail |
| Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. | DisGeNET | Detail |
| Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loc... | DisGeNET | Detail |
| Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. | DisGeNET | Detail |
| NA | DisGeNET | Detail |
Overlapped Transcript Coordinates
| Gene | Transcript ID | Exon Number | Chromosome | Start | Stop | Type | Amino Mutation | Transcript Position | Links |
|---|
Overlapped Transcript
| Gene | Transcript ID | Chromosome | Start | Stop | Links |
|---|
- Gene
- -
- dbSNP
- rs3764147 dbSNP
- Genome
- hg38
- Position
- chr13:43,883,789-43,883,789
- Variant Type
- snv
- Reference Allele
- A
- Alternative Allele
- G
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1190
- Mean of sample read depth (HGVD)
- 36.50
- Standard deviation of sample read depth (HGVD)
- 18.15
- Number of reference allele (HGVD)
- 1596
- Number of alternative allele (HGVD)
- 784
- Allele Frequency (HGVD)
- 0.32941176470588235
- Gene Symbol (HGVD)
- LACC1
- ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- PASS
- Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- rs3764147
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.3358
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 5628
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8648
- East Asian Allele Counts (ExAC)
- 2695
- East Asian Heterozygous Counts (ExAC)
- 1885
- East Asian Homozygous Counts (ExAC)
- 405
- East Asian Allele Frequency (ExAC)
- 0.3116327474560592
- Chromosome Counts in All Race (ExAC)
- 121148
- Allele Counts in All Race (ExAC)
- 32735
- Heterozygous Counts in All Race (ExAC)
- 23305
- Homozygous Counts in All Race (ExAC)
- 4715
- Allele Frequency in All Race (ExAC)
- 0.27020668933866016
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